Space-Efficient Representation of Genomic k-Mer Count Tables

DOI10.4230/LIPICS.WABI.2021.8MaRDI QIDQ6133870zbMATH OpenOpenAlexFDO

Authors Djamal Belazzougui, Gregory Kucherov

Publication date 24 July 2023

Full work available at URL https://hal.science/hal-03447152

zbMATH Keywords

\(k\)-mer countingBloom filtercompressed static functioncompressiondata structuresempirical entropyminimizers

Mathematics Subject Classification ID

Computational methods for problems pertaining to biology (92-08) Genetics and epigenetics (92D10) Protein sequences, DNA sequences (92D20)

Recommendations

• Disk compression of k-mer sets
• Representation of \(k\)-mer sets using spectrum-preserving string sets
• Compression of Multiple k-Mer Sets by Iterative SPSS Decomposition
• Effective parallel multicore-optimized k-mers counting algorithm
• Succinct de Bruijn graphs

Cited in

(6)

• Effective parallel multicore-optimized k-mers counting algorithm
• Representation of \(k\)-mer sets using spectrum-preserving string sets
• Compression of Multiple k-Mer Sets by Iterative SPSS Decomposition
• Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time
• On weighted k-mer dictionaries
• Fast gapped k-mer counting with subdivided multi-way bucketed cuckoo hash tables

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